Variant 11-117428322-CG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_020693.4(DSCAML1):c.*5del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,482,852 control chromosomes in the GnomAD database, including 13 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0048 ( 6 hom., cov: 31)

Exomes 𝑓: 0.00099 ( 7 hom. )

Consequence

DSCAML1
NM_020693.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.95

Variant links:

Genes affected

DSCAML1 (HGNC:14656): (DS cell adhesion molecule like 1) The protein encoded by this gene is a member of the Ig superfamily of cell adhesion molecules and is involved in neuronal differentiation. The encoded membrane-bound protein localizes to the cell surface, where it forms aggregates that repel neuronal processes of the same cell type. [provided by RefSeq, Sep 2016]

DSCAML1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant 11-117428322-CG-C is Benign according to our data. Variant chr11-117428322-CG-C is described in ClinVar as [Benign]. Clinvar id is 3037184.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 728 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSCAML1	NM_020693.4 linkuse as main transcript	c.*5del		3_prime_UTR_variant	33/33	ENST00000651296.2	NP_065744.3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSCAML1	ENST00000651296.2 linkuse as main transcript	c.*5del	3_prime_UTR_variant	33/33		NM_020693.4	ENSP00000498769		Q8TD84-1
DSCAML1	ENST00000321322.6 linkuse as main transcript	c.*5del	3_prime_UTR_variant	33/33	1		ENSP00000315465	P1
DSCAML1	ENST00000527706.5 linkuse as main transcript	c.*5del	3_prime_UTR_variant	31/31	5		ENSP00000434335		Q8TD84-2
DSCAML1	ENST00000651172.1 linkuse as main transcript		downstream_gene_variant				ENSP00000498407	P1

Frequencies

GnomAD3 genomes

AF:

0.00475

AC:

723

AN:

152096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00733

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000500

Gnomad OTH

AF:

0.00764

GnomAD3 exomes

AF:

0.00166

AC:

378

AN:

227122

Hom.:

AF XY:

0.00145

AC XY:

181

AN XY:

125108

show subpopulations

Gnomad AFR exome

AF:

0.0132

Gnomad AMR exome

AF:

0.00381

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000365

Gnomad FIN exome

AF:

0.0000474

Gnomad NFE exome

AF:

0.000618

Gnomad OTH exome

AF:

0.00327

GnomAD4 exome

AF:

0.000994

AC:

1323

AN:

1330638

Hom.:

Cov.:

AF XY:

0.000948

AC XY:

633

AN XY:

667482

show subpopulations

Gnomad4 AFR exome

AF:

0.0140

Gnomad4 AMR exome

AF:

0.00407

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000738

Gnomad4 FIN exome

AF:

0.0000384

Gnomad4 NFE exome

AF:

0.000576

Gnomad4 OTH exome

AF:

0.00231

GnomAD4 genome

AF:

0.00478

AC:

728

AN:

152214

Hom.:

Cov.:

AF XY:

0.00464

AC XY:

345

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0135

Gnomad4 AMR

AF:

0.00732

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.000500

Gnomad4 OTH

AF:

0.00756

Alfa

AF:

0.00308

Hom.:

Bravo

AF:

0.00584

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DSCAML1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 03, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over